The scoring system is going to be interesting to say the least, awarding bonus points for in season promotions and weighting statistical goals based on the level of competition (AAA vs Rookie Ball for instance). It also weights professional metrics that scouts covet (K/BB ratio, Slug %, etc) over traditional stats like ERA.

Im just wondering for guys like Skaggs and Bundy how will they be scored if they get promoted back to the big leagues.... or will they just drop off...

Yeah, they will need to clarify that. Fantasy leagues/promotions like this always favor a certain subset of player - i.e. pitcher vs. hitter, starter vs. reliever, slugger vs. speed guy - it will be interesting to see how this scoring plays out in real time.